Admin: Pierre Lindenbaum

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Posts by Pierre Lindenbaum

<prev • 8,551 results • page 2 of 856 • next >
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Answer: A: Cannot create the sorted sam using samtools sort
... > Error: samtools sort: couldn't allocate memory for bam_mem use option -m `(-m INT Set maximum memory per thread; suffix K/M/G recognized [768M])` to reduce the memory. For example : '-m 10M' but it looks like your computer hasn't enough memory... ...
written 5 days ago by Pierre Lindenbaum121k
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Answer: A: InterProScan java issue
... in https://github.com/ebi-pf-team/interproscan/blob/ff63535bfdaba64f9b48fc0c505f2ade85bd9d64/core/jms-implementation/support-mini-x86-32/interproscan.sh#L31 if [[ "${JAVA_MAJOR_VERSION}" == "1" && "${JAVA_MINOR_VERSION}" -lt "8" ]]; checks that the first number is '1" (like in "1.8") b ...
written 5 days ago by Pierre Lindenbaum121k
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Answer: A: biological formats format converter script
... https://github.com/bioconvert/bioconvert (python) > Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another. ...
written 5 days ago by Pierre Lindenbaum121k
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Comment: C: Pipe SamToFastq, BWA mem not working
... > I'm about to give up and just run each command separately, give `samtools collate | samtools fastq` a try. ...
written 5 days ago by Pierre Lindenbaum121k
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Comment: C: Python - finding INDELS and SNPS
... cited in > Complete chloroplast genomes of medicinally important Teucrium species and comparative analyses with related species from Lamiaceae https://media.proquest.com/media/hms/PFT/1/PIi9A?_s=oXllOyF0mU%2BY2Zya4BZ5dUOHgNI%3D ...
written 6 days ago by Pierre Lindenbaum121k
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Comment: C: samtools depth for multiple files
... https://github.com/samtools/samtools/blob/develop/bam2depth.c#L84 ...
written 6 days ago by Pierre Lindenbaum121k
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Comment: A: Is it possible to directly convert fastq to CRAM ?
... I would say 'no' because CRAM needs a reference genome to store its' bases, hence the reads need to be mapped. what ATpoint said :-) ...
written 6 days ago by Pierre Lindenbaum121k
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Comment: C: samtools depth for multiple files
... you version of samtools is too old. http://www.htslib.org/doc/samtools.html $ samtools depth Usage: samtools depth [options] in1.bam [in2.bam [...]] Options: (...) -H print a file header (...) $ samtools Program: samtools (Tools for alignments ...
written 6 days ago by Pierre Lindenbaum121k
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Answer: A: samtools depth for multiple files
... samtools depth -H src/jvarkit-git/src/test/resources/S*.bam | awk -F '\t' '(NR==1) {split($0,header);N=0.0;next;} {N++;for(i=3;i<=NF;i++) a[i]+=int($i);} END { for(x in a) print header[x], a[x]/N;}' src/jvarkit-git/src/test/resources/S2.bam 7.55906 src/jvarkit-git/src/test/reso ...
written 6 days ago by Pierre Lindenbaum121k
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Comment: C: ensembl VEP: gnomAD genome annotation <AF1>&<AF2>
... I would have say that there are two alternative alleles at this position, or two values for genomes and exomes, but I don't even find the same AF values at that position in gnomad... ...
written 7 days ago by Pierre Lindenbaum121k

Latest awards to Pierre Lindenbaum

Teacher 2 days ago, created an answer with at least 3 up-votes. For A: Plotting Density Of Snps On Chromosomes
Scholar 4 days ago, created an answer that has been accepted. For A: how to edit a fasta file
Scholar 4 days ago, created an answer that has been accepted. For A: how to edit a fasta file
Commentator 4 days ago, created a comment with at least 3 up-votes. For C: Pipe SamToFastq, BWA mem not working
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: How To Retrieve Reads Supporting A Snp/Indel
Teacher 9 days ago, created an answer with at least 3 up-votes. For A: How To Retrieve Reads Supporting A Snp/Indel
Scholar 10 days ago, created an answer that has been accepted. For A: how to edit a fasta file
Scholar 10 days ago, created an answer that has been accepted. For A: how to edit a fasta file
Good Answer 10 days ago, created an answer that was upvoted at least 5 times. For A: how to edit a fasta file
Teacher 11 days ago, created an answer with at least 3 up-votes. For A: How To Retrieve Reads Supporting A Snp/Indel
Teacher 11 days ago, created an answer with at least 3 up-votes. For A: How To Retrieve Reads Supporting A Snp/Indel
Teacher 16 days ago, created an answer with at least 3 up-votes. For A: Ncbi Tax Id For Draft Bacteria Genomes
Teacher 16 days ago, created an answer with at least 3 up-votes. For A: Ncbi Tax Id For Draft Bacteria Genomes
Scholar 16 days ago, created an answer that has been accepted. For C: BED file : error in naming chromosome's column
Appreciated 18 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Teacher 19 days ago, created an answer with at least 3 up-votes. For A: Ncbi Tax Id For Draft Bacteria Genomes
Popular Question 22 days ago, created a question with more than 1,000 views. For samtools 1.0 'index' : CSI index vs BAI index ?
Appreciated 23 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Scholar 24 days ago, created an answer that has been accepted. For C: BED file : error in naming chromosome's column
Teacher 25 days ago, created an answer with at least 3 up-votes. For A: Ncbi Tax Id For Draft Bacteria Genomes
Commentator 26 days ago, created a comment with at least 3 up-votes. For C: Introduction To Genomics For Non-Biologists Willing To Become Bioinformaticians
Appreciated 26 days ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org
Good Answer 28 days ago, created an answer that was upvoted at least 5 times. For A: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
Scholar 4 weeks ago, created an answer that has been accepted. For C: BED file : error in naming chromosome's column
Appreciated 4 weeks ago, created a post with more than 5 votes. For Biostars based Q&A for Bioconductor: http://support.bioconductor.org

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